•Investigate resource sharing and payoff allocation in a three-stage system.•Integrate network DEA and Shapley value method for payoff allocation.•Prove cooperative games among stages in a three-stage system is superadditive.•Allocate the increased profit gained from resource sharing by the Shapley value method.•This new method is demonstrated by an illustrative example. Resource sharing exists not only among multiple entities but also among various stages of a single network structure system. Previous studies focused on how to allocate total given sharable resources to stages to maximize the efficiency of the network structure system, and a few discussed the fair allocation of potential gains obtained from resource sharing. In this study, we explore a new case in which the common inputs (or shared resources) of all stages are known. By constructing a game that regards each stage as a player, we integrate cooperative game theory with network data envelopment analysis (DEA) to explore the payoff allocation problem in a three-stage system. We build network DEA models to calculate the optimal profits of the system before and after resource sharing (i.e., pre- and post-collaboration optimal profits), and then apply the Shapley value method to allocate the increased profits of the system to its stages. Results indicate that the game among stages in a three-stage system is superadditive. A numerical example is provided to illustrate our method.